DISVIS

Recommended Workflow

In contrast to Docking applications DisVis is aimed at explorative modeling, i.e. checking data-consistency and information content of distance restraints intented to directly design follow up studies or to generate a filtered restraint set to drive molecular Docking e.g. with HADDOCK.
A typical DisVis investigation thus should start with determining the consistency of the restraints dataset using the “quick scanning” option. After inspecting the results, the dataset can be filtered to discard false-positive restraints using the violation analysis. When the consistency of the dataset has been secured, additional runs can be performed with the “complete scanning” setting and optionally targeted interface analysis. With the resulting information, interface residues can be inferred and through the occupancy analysis the putative binding pose of the ligand can be approximated. These insights are of use in determining future experiments to further characterize the interaction.

Input

Fixed chain:

a file in pdb or mmCIF format containing the coordinates of the fixed chain which will be kept stationary during the search of the accessible interaction space.

Scanning chain:

a file in pdb or mmCIF format containing the coordinates of the scanning chain which will be moved during the search of the accessible interaction space.

NOTE: Selecting the smaller interaction partner as scanning chain speeds up the calculation. However, the density map of the accessible interaction space is only provided for the fixed chain.

Restrains file:

a text-file containing the distance restraints in the following format:

<chainid 1> <resid 1> <atomname 1> <chainid 2> <resid 2> <atomname 2> <mindist> <maxdist>

As an example:

A 18 CA F 27 CB 10.0 20.0

The first selection (here "A 18 CA") must correspond to the fixed chain and the second selection (here "F 27 CB") the scanning chain.
This puts a distance restraint between the CA-atom of residue 18 of chain A of the fixed chain and the CB-atom of residue 27 of chain F of the scanning chain that should be longer than or equal to 10A and smaller than or equal to 20A. Comments can be added by starting the line with the pound sign (#) while empty lines are ignored.

Interaction analysis (Residue selection):

The interaction analysis can be performed to determine which residues are most likely at the interface. For this a a plain text file needs to be provided specifying the residue numbers of the fixed and scanning chain for which the interaction analysis should be performed. The input file consists of two lines, where the two lines are a space separated sequence of residue numbers with the first line corresponding to the fixed chain and the second line corresponding to the scanning chain. As the interaction analysis is particularly expensive, only complexes consistent with all-3 up to all restraints are considered.

NOTE: It is advised to perform a "quick scanning" without the interface analysis first to ascertain that complexes consistent with all-3 restraints exist.

A simple example for the selection-file:

1 2 3 4
101 302 888

This will select residue numbers 1, 2, 3, and 4 for the fixed and 101, 302, and 888 for the scanning chain.

Occupancy analysis:

It is possible to perform a grid occupancy analysis for complexes consistent with all-3 up to all number of restraints by activating this option on the submission page. This will produce a density map in the coordinate space of the fixed chain giving a normalized indication of how frequent a grid point is occupied by any atom of the scanning chain.

Tag:

A custom tag to identify your run. Supported characters: a-z A-Z 0-9 _ + - = / , . :

Parameters:

• Rotational sampling interval - Rotational sampling density in degrees
• Voxel spacing - Voxel spacing of search grid in angstrom
• Interaction radius - Radius of the interaction space for each atom in angstrom. Atoms are thus considered interacting if the distance is larger than the vdW radius and shorther than or equal to vdW + interaction_radius
• Maximum clash volume - Maximum allowed volume of clashes. Increasing this number results in more allowed complexes.
• Minimum interaction volume - Minimal required interaction volume for a conformation to be considered a complex. Increasing this number results in a stricter counting of complexes.

Output

accessible_complexes.out:

a text file containing the number of complexes consistent with a given number of restraints. Column 1 shows the number of consistent restraints for each complex counted, denoted by N; column 2 shows the number of complexes consistent with exactly N restraints; column 3 shows the fraction of all complexes sampled that are consistent with exactly N restraints; column 4 gives the number of complexes consistent with at least N restraints, and is thus the cumulative sum of column 2; column 5 is again the fraction of complexes consistent with at least N restraints, and also the cumulative sum of column 3.

violations.out:

a text file showing how often a specific restraint is violated for complexes consistent with a number of restraints. The higher the violation fraction of a specific restraint, the more likely it is to be a false-positive. Column 1 shows the number of consistent restraints N, while each following column indicates the violation fractions of a specific restraint for complexes consistent with at least N restraints. Each row thus represents the fraction of all complexes consistent with at least N restraints that violated a particular restraint.

accessible_interaction_space.mrc:

a density file in MRC format. The density represents the center of mass of the scanning chain conforming to the maximum found consistent restraints at every position in space. The density can be inspected by opening it together with the fixed chain in a molecular viewer.

z-score.out:

a text file giving the z-score for each restraint. The higher the score, the more likely the restraint is a false-positive. Z-scores above 1.0 are explicitly mentioned in the output. The first column indicates the restraint; column 2 gives the average violation fraction, i.e. the average of the corresponding column in violations.out; column 3 represents the standard deviation of the average violation fraction; and column 4 finally gives the z-score.

disvis.log:

a log file showing all the parameters used, together with date and time indications.

If an occupancy and/or interaction analysis was requested, disvis also outputs the following files:

occupancy_N.mrc:

a volume file giving a normalized indication of how frequent a grid point is occupied by the ligand, where N indicates the minimal required number of consistent restraints that resulted in the occupancy grid.

[receptor|ligand]_interactions.txt:

a text file containing the average number of interactions per complex for each selected residue made, for both the fixed (receptor) and scanning chain (ligand). Each column denotes the minimal number of consistent restraints of each complex for which interactions were counted.

Visualizing the accessible interaction space/occupancy analysis

The accessible interaction space consistent with at least N restraints as well as the density maps of the occupancy analysis can be visualized by opening the fixed chain (fixed_chain.pdb) used in the disvis run together with the accessible_interaction_space.mrc/occupancy_N.mrc output file with UCSF Chimera. The density slider in Chimera can be adjusted to change N.

Help/Contact

If you have further questions or run into issues submitting your data, please contact us at disvis.server[at]gmail.com.